This sounds like the same problem the SV650s had (have?). If memory serves, there's a small drain hole in the sparkplug well to let out excess water -- it's very common for the hole to get plugged and so the sparkplug looses connection.
I had this problem with my SV for a quite a while, and lemme tell ya, loosing a cylinder at 70mph SUCKS. For my SV, even a light misting seemed to be enough to screw stuff up. Never did get the problem quite resolved (wound up getting my Speedy), and thankfully haven't had any such problems since.
Doesn't make me happy to hear the Bonnie mills are subject to the same squirrelyness. You'd think that an English bike would be designed with rain riding in mind!
--Jaeger
